From 89fa2376b049e1a94fd6d820c223a2d909fbfbd4 Mon Sep 17 00:00:00 2001 From: Ian Taylor Date: Thu, 24 Oct 2024 16:55:42 -0700 Subject: [PATCH 1/6] improve description of hermaphroditism --- 9control.tex | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/9control.tex b/9control.tex index 10ce882e..c7d3e3cd 100644 --- a/9control.tex +++ b/9control.tex @@ -682,23 +682,23 @@ \multicolumn{2}{l}{COND = 1 or} \Tstrut & \\ \multicolumn{2}{l}{COND = -1} & Read 2 lines below if hermaphroditism is selected. Also read 3 parameters after reading the male (option 1) or female (option -1) weight-length parameter. \Bstrut\\ - & -1.2 & Hermaphroditism Season: \\ - & & -1 to do transition at the end of each season (after mortality and before movement); and \\ + & -1.2 & Hermaphroditism Season / First Age: \\ + & & -1 to do transition at the end of each season (after mortality and before movement); or \\ & & to select just one season. \\ & & If fractional part included (optional), indicates first age that transitions (otherwise, age 1 assumed). \\ - & 0.5 & Include males in spawning biomass; \\ + & 0.5 & Fraction of males to include in spawning biomass; \\ & & 0 = no males in spawning biomass; \\ - & > 0 & < 1 = fraction of male biomass to include in spawning biomass; and \\ + & & fraction of male biomass to include in spawning biomass; and \\ & & 1 = simple addition of males to females. \Bstrut\\ \hline \end{longtable} \vspace*{-\baselineskip} -The hermaphroditism option requires three full parameter lines in the mortality growth section: +The hermaphroditism option requires three full parameter lines in the mortality and growth section. These parameters control a cumulative normal distribution function as follows: \begin{enumerate} - \item A parameter line for inflection point (in age) at when fish may begin to change sex. - \item The standard deviation. - \item The asymptote of the maximum proportion that will transition to the other sex + \item The inflection point where the transition rate is halfway from 0 to the asymptote. + \item The standard deviation of the cumulative normal (such that about 95\% of the increase in transition rate occurs within 2 standard deviations of the inflection point). + \item The asymptote (the maximum proportion that will transition to the other sex in a time step). \end{enumerate} These parameter lines are entered directly after the weight-at-length parameters for males. From 3e7079cafbe73903545e97b7212b0286e6deb561 Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Mon, 28 Oct 2024 11:34:31 -0400 Subject: [PATCH 2/6] Update 9control.tex with hyperlink between two hermaphrodite parameter sections --- 9control.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/9control.tex b/9control.tex index c7d3e3cd..4a56202e 100644 --- a/9control.tex +++ b/9control.tex @@ -694,7 +694,7 @@ \end{longtable} \vspace*{-\baselineskip} -The hermaphroditism option requires three full parameter lines in the mortality and growth section. These parameters control a cumulative normal distribution function as follows: +The hermaphroditism option requires three full parameter lines in the \hyperlink{HermaphroditeBiology}{mortality growth section}. These parameters control a cumulative normal distribution function as follows: \begin{enumerate} \item The inflection point where the transition rate is halfway from 0 to the asymptote. \item The standard deviation of the cumulative normal (such that about 95\% of the increase in transition rate occurs within 2 standard deviations of the inflection point). @@ -862,7 +862,7 @@ \subsubsection{Predator Fleet Mortality} \multicolumn{2}{l}{COND: growth pattern > 1} \Tstrut & Repeat male parameters in the above order for growth pattern 2. \\ \hline - \multicolumn{2}{l}{COND: Hermaphroditism} \Tstrut & 3 parameters lines define a normal distribution for the transition rate of females to males (or vice versa). \\ + \multicolumn{2}{l}{\hypertarget{HermaphroditeBiology}{COND: Hermaphroditism}} \Tstrut & 3 parameters lines define a normal distribution for the transition rate of females to males (or vice versa). \\ & Inflect Age & Hermaphrodite inflection age. \\ & \gls{sd} & Hermaphrodite standard deviation (in age). \\ & Asmp Rate & Hermaphrodite asymptotic rate. \Bstrut\\ From f7020209c5c0001270969add8b4b066a8e2df407 Mon Sep 17 00:00:00 2001 From: Elizabeth Perl Date: Mon, 28 Oct 2024 11:36:39 -0400 Subject: [PATCH 3/6] Update dictionary.txt with HermaphroditeBiology --- dictionary.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/dictionary.txt b/dictionary.txt index a2eb6cef..443159ec 100644 --- a/dictionary.txt +++ b/dictionary.txt @@ -226,6 +226,7 @@ GradLo GrowthCessation groundfish Hamel +HermaphroditeBiology Hermaphroditism hermaphroditism hess From 78dc96fffda4de9421f0c7fff873014ce1623788 Mon Sep 17 00:00:00 2001 From: Ian Taylor Date: Mon, 28 Oct 2024 13:52:58 -0700 Subject: [PATCH 4/6] refine descriptions of the hermaphroditism settings --- 9control.tex | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/9control.tex b/9control.tex index 4a56202e..c2747fba 100644 --- a/9control.tex +++ b/9control.tex @@ -677,7 +677,7 @@ & & 0 = not used; \\ & & 1 = invoke female to male age-specific function; and \\ & & -1 = invoke male to female age-specific function. \\ - & & Note: this creates the annual, age-specific fraction that change sex, it is not the fraction that is each sex. \Bstrut\\ + & & Note: this creates the annual, age-specific fraction that change sex, it is not the fraction that is each sex. Also, the fraction female parameter should be configured to reflect the fraction of age 0 fish. Values of 0 or 1 may lead to NaN likelihoods, so we recommend changing values that would be fixed at 0 or 1 to 0.000001 or 0.999999.\Bstrut\\ \hline \multicolumn{2}{l}{COND = 1 or} \Tstrut & \\ @@ -694,11 +694,11 @@ \end{longtable} \vspace*{-\baselineskip} -The hermaphroditism option requires three full parameter lines in the \hyperlink{HermaphroditeBiology}{mortality growth section}. These parameters control a cumulative normal distribution function as follows: +The hermaphroditism option requires three full parameter lines in the \hyperlink{HermaphroditeBiology}{mortality and growth section}. These parameters control a cumulative normal distribution function as follows: \begin{enumerate} - \item The inflection point where the transition rate is halfway from 0 to the asymptote. + \item The inflection age where the transition rate is halfway from 0 to its asymptote. \item The standard deviation of the cumulative normal (such that about 95\% of the increase in transition rate occurs within 2 standard deviations of the inflection point). - \item The asymptote (the maximum proportion that will transition to the other sex in a time step). + \item The asymptotic transition rate (the highest proportion that will transition to the other sex in a time step). \end{enumerate} These parameter lines are entered directly after the weight-at-length parameters for males. @@ -862,10 +862,10 @@ \subsubsection{Predator Fleet Mortality} \multicolumn{2}{l}{COND: growth pattern > 1} \Tstrut & Repeat male parameters in the above order for growth pattern 2. \\ \hline - \multicolumn{2}{l}{\hypertarget{HermaphroditeBiology}{COND: Hermaphroditism}} \Tstrut & 3 parameters lines define a normal distribution for the transition rate of females to males (or vice versa). \\ - & Inflect Age & Hermaphrodite inflection age. \\ - & \gls{sd} & Hermaphrodite standard deviation (in age). \\ - & Asmp Rate & Hermaphrodite asymptotic rate. \Bstrut\\ + \multicolumn{2}{l}{\hypertarget{HermaphroditeBiology}{COND: Hermaphroditism}} \Tstrut & 3 parameters lines define a cumulative normal distribution for the transition rate of females to males (or vice versa). For more detail on these parameters, see the description \hyperlink{Hermaphroditism}{Hermaphroditism controls} above.\\ + & Inflect Age & Hermaphrodite inflection age where the transition rate is halfway from 0 to its asymptote. \\ + & \gls{sd} & Hermaphrodite standard deviation of the cumulative normal. \\ + & Asmp Rate & Hermaphrodite asymptotic transition rate. \Bstrut\\ \hline \multicolumn{2}{l}{COND: Recruitment Distribution} \Tstrut & 3 parameters lines defining recruitment distribution. See \hyperlink{recdist}{Recruitment Distribution and Parameters} for more details about recruitment apportionment parameterization. \\ From 40edc2fad0d951525e535d9415769571fd264d14 Mon Sep 17 00:00:00 2001 From: Ian Taylor Date: Mon, 28 Oct 2024 14:27:04 -0700 Subject: [PATCH 5/6] fix incorrect description of where parameter lines are located --- 9control.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/9control.tex b/9control.tex index c2747fba..fa8304a7 100644 --- a/9control.tex +++ b/9control.tex @@ -681,7 +681,7 @@ \hline \multicolumn{2}{l}{COND = 1 or} \Tstrut & \\ - \multicolumn{2}{l}{COND = -1} & Read 2 lines below if hermaphroditism is selected. Also read 3 parameters after reading the male (option 1) or female (option -1) weight-length parameter. \Bstrut\\ + \multicolumn{2}{l}{COND = -1} & Read 2 lines below if hermaphroditism is selected. Also read 3 parameters after reading the male weight-length parameters. \Bstrut\\ & -1.2 & Hermaphroditism Season / First Age: \\ & & -1 to do transition at the end of each season (after mortality and before movement); or \\ & & to select just one season. \\ From 21ef32a27a3f32954bcfbd0b4bb0f522e670e102 Mon Sep 17 00:00:00 2001 From: Ian Taylor Date: Tue, 29 Oct 2024 09:40:45 -0700 Subject: [PATCH 6/6] add intro paragraph to hermaphroditism section --- 9control.tex | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/9control.tex b/9control.tex index fa8304a7..96013708 100644 --- a/9control.tex +++ b/9control.tex @@ -657,6 +657,10 @@ \hypertarget{Hermaphroditism}{} \subsubsection[Hermaphroditism]{\protect\hyperlink{Hermaphroditism}{Hermaphroditism}} +Sequential hermaphroditism can be modeled in Stock Synthesis by having recruits be all female or all male and then defining a 3-parameter function which represents the annual age-specific probability of transition to the other sex. In a seasonal model, the transition can occur after each season or just once per year. There are also settings to control the first age which transitions and the contribution of males to the spawning biomass calculations. + +The \hyperlink{SexRatio}{fraction female} parameter should be configured to reflect the fraction of age 0 fish of each sex. Values of 0 or 1 may lead to NaN likelihoods, so we recommend changing values that would be fixed at 0 or 1 to 0.000001 or 0.999999. + \begin{longtable}{p{0.5cm} p{2cm} p{13cm}} \hline \multicolumn{2}{l}{Typical Value} & Description and Options \Tstrut\Bstrut\\ @@ -675,9 +679,8 @@ 0 & & Hermaphroditism Option: \Tstrut\\ & & 0 = not used; \\ - & & 1 = invoke female to male age-specific function; and \\ - & & -1 = invoke male to female age-specific function. \\ - & & Note: this creates the annual, age-specific fraction that change sex, it is not the fraction that is each sex. Also, the fraction female parameter should be configured to reflect the fraction of age 0 fish. Values of 0 or 1 may lead to NaN likelihoods, so we recommend changing values that would be fixed at 0 or 1 to 0.000001 or 0.999999.\Bstrut\\ + & & 1 = invoke female-to-male age-specific function; and \\ + & & -1 = invoke male-to-female age-specific function.\Bstrut\\ \hline \multicolumn{2}{l}{COND = 1 or} \Tstrut & \\